Functional enrichment analysis

library(topGO)
library(knitr)   # to use kable()
library(limma)   # to use vennDiagram()
library(ggplot2)
TAG <- params$TAG
VAR <- params$VAR
ANNOTATION <- list(genes = '../2019-07-26/genes/annotation.txt',
                   isoforms = '../2019-07-26/transcripts/annotation.txt')
TAGDIR <- paste0('../2020-01-08/', TAG, '/')

Introduction

This is the enrichment analysis for isoforms regulated by hatching. Because I quantified the association of expression with hatching in two different ways, this document has two sections. Section Variance reports the enrichment analysis performed with isoforms ordered by the proportion of expression variance explained by hatching. Note that some isoforms with low variance may still be highly associated with hatching, even if the fold change between levels of this factor is low. Section Differential expression uses an ordering of isoforms based on the significance of the differential expression between levels of hatching, which does depend on fold change.

Reading the data

Functional annotation is in 2019-07-26. I will also upload two lists of isoforms, with either proportion of variance explained by hatching or p-value of differential expression test.

tagVariance <- read.table(paste0(TAGDIR, VAR, '_variance.txt'))
tagPValue   <- read.table(paste0(TAGDIR, VAR, '_pvalue.txt'))
annotation  <- read.table(ANNOTATION[[TAG]], col.names = c('tagname', 'goterms'))

To initialize the topGOdata object, I will need the gene list as a named numeric vector, where the names are the isoforms identifiers and the numeric values, either the portion of variance explained by hatching or the p-values of the differential expression test. The structure() function adds attributes to an object.

Variance <- structure(tagVariance[,1], names = row.names(tagVariance))
PValues  <- structure(tagPValue[,1],   names = row.names(tagPValue))
rm(tagVariance, tagPValue)

There are 33037 isoforms scored with a variance portion and a differential expression p-value. It should actually be the exact same isoforms. The annotation data frame has more than one GO term for every tag, separated by |. I need a named list.

head(annotation)

##          tagname
## 1 TCONS_00000002
## 2 TCONS_00000010
## 3 TCONS_00000011
## 4 TCONS_00000016
## 5 TCONS_00000017
## 6 TCONS_00000018
##                                                             goterms
## 1                                  GO:0008417|GO:0016020|GO:0006486
## 2                                  GO:0043130|GO:0005515|GO:0043161
## 3                       GO:0005840|GO:0015935|GO:0003735|GO:0006412
## 4 GO:0006355|GO:0003700|GO:0006357|GO:0043565|GO:0005634|GO:0032502
## 5 GO:0006355|GO:0003700|GO:0006357|GO:0043565|GO:0005634|GO:0032502
## 6 GO:0006355|GO:0003700|GO:0006357|GO:0043565|GO:0005634|GO:0032502

allgenes2GO <- strsplit(as.character(annotation$goterms), "|", fixed = TRUE)
names(allgenes2GO) <- annotation$tagname
rm(annotation)

There are 19735 isoforms with GO annotations. But the differential expression analysis includes many more isoforms. In order to include the not-annotated isoforms in the enrichment analysis, to see if annotated or not annotated isoforms are more or less often differentially expressed, I should attribute a GO term to them. According to [http://geneontology.org/docs/faq/] nowadays we express lack of annotation by annotating to the root nodes, i.e. GO:0008150 biological_process, GO:0003674 molecular_function, and GO:0005575 cellular_component.

for (tag in unique(c(names(PValues), names(Variance)))) {
   if (! tag %in% names(allgenes2GO)) {
      allgenes2GO <- append(allgenes2GO,
         structure(list(c("GO:0008150", "GO:0003674", "GO:0005575")), names = tag))
   }
}

Using differential expression p-values

Building the topGO object

Creation of a topGO dataset is documented in section 4 of topGO’s the user manual: https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf. I need to use the new command, and fill up the slots. The annot object must be a function that compiles “a list of GO terms such that each element in the list is a character vector containing all the gene identifiers that are mapped to the respective GO term.” There are several options, that you can check using help(annFUN.gene2GO), for example. The annFUN.gene2GO requires a gene2GO argument, which is the list of gene-to-GO terms I made before. The geneSelectionFun object is a function that selects the interesting (most significant) genes. It is required to perform Fisher’s exact test. The nodeSize is used to prune the GO hierarchy from the terms which have less than n annotated genes.

I generate three datasets, to analyse each of the three ontologies.

selection <- function(allScores) {return(allScores < 0.05)}
GOdata.BP <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'BP', 
   allGenes = PValues,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

GOdata.MF <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'MF',
   allGenes = PValues,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

GOdata.CC <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'CC',
   allGenes = PValues,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

DataSummary <- data.frame(ontology = c('BP', 'MF', 'CC'),
   Num_Genes = sapply(list(GOdata.BP, GOdata.MF, GOdata.CC), numGenes),
   Num_GO_terms = sapply(list(GOdata.BP, GOdata.MF, GOdata.CC), function(x) length(usedGO(x))))
kable(DataSummary, caption='Number of feasible genes or transcripts and number of GO terms used in each data set.')
rm(DataSummary)

Number of feasible genes or transcripts and number of GO terms used in each data set.

ontology	Num_Genes	Num_GO_terms
BP	26235	1582
MF	30580	791
CC	21616	390

Running the tests

There are more than one way to test for enrichment. Something that took me a while to understand is that not only there are different test statistics (Fisher’s exact test, Kolmogorov-Smirnov, and others) but also different algorithms: classic, elim, weight… The algorithms are ways to deal with the dependence structure among GO terms due to topology. Some algorithms are compatible with all statistics implemented in topGO. But the weight and the parentchild algorithms are only applicable to Fisher’s exact test. I am not interested in the classic algorithm, which treats GO nodes as independent, and therefore produces an excess of significant results. I will not use the Fisher’s exact test, because it dependes on an arbitrary threshold of significance on non-adjusted p-values.

BP.elim     <- runTest(GOdata.BP, algorithm = "elim",     statistic = "ks")
BP.weight01 <- runTest(GOdata.BP, algorithm = "weight01", statistic = "ks")
BP.lea      <- runTest(GOdata.BP, algorithm = "lea",      statistic = "ks")
MF.elim     <- runTest(GOdata.MF, algorithm = "elim",     statistic = "ks")
MF.weight01 <- runTest(GOdata.MF, algorithm = "weight01", statistic = "ks")
MF.lea      <- runTest(GOdata.MF, algorithm = "lea",      statistic = "ks")
CC.elim     <- runTest(GOdata.CC, algorithm = "elim",     statistic = "ks")
CC.weight01 <- runTest(GOdata.CC, algorithm = "weight01", statistic = "ks")
CC.lea      <- runTest(GOdata.CC, algorithm = "lea",      statistic = "ks")

ResultsSummary <- data.frame(ontology = rep(c("BP", "MF", "CC"), each = 3),
   algorithm = rep(c("elim", "weight01", "lea"), 3),
   TermsTested = sapply(list(BP.elim, BP.weight01, BP.lea, MF.elim, MF.weight01, MF.lea, CC.elim, CC.weight01, CC.lea), function(X) length(score(X))),
   Significant = sapply(list(BP.elim, BP.weight01, BP.lea, MF.elim, MF.weight01, MF.lea, CC.elim, CC.weight01, CC.lea), function(X) sum(score(X) < 0.01)))

kable(ResultsSummary, caption="Number of non-trivial terms tested and those with a score (not corrected p-value) lower than 0.01.")

Number of non-trivial terms tested and those with a score (not corrected p-value) lower than 0.01.

ontology	algorithm	TermsTested	Significant
BP	elim	1582	24
BP	weight01	1582	10
BP	lea	1582	37
MF	elim	791	10
MF	weight01	791	13
MF	lea	791	13
CC	elim	390	2
CC	weight01	390	1
CC	lea	390	3

rm(ResultsSummary)

Results

The topGO package does not pay much attention to what terms are significant because they are overrepresented and which ones are underrepresented among the most differentially expressed genes. I think it’s worth separating them, to facilitate the biological interpretation. Note that not all terms listed in the tables below are significant. The scores for the three methods (elim, weight01 and lea) are non-corrected p-values.

Biological process

orderedTerms <- names(sort(score(BP.weight01)))
significant.weight01 <- score(BP.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(BP.lea)[orderedTerms] <= 0.01
significant.elim     <- score(BP.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
BP.pvalue.sigTerms <- sigTerms

BP.all <- GenTable(GOdata.BP, elim=BP.elim, weight01=BP.weight01, lea=BP.lea,
                   orderBy="weight01", ranksOf="elim", topNodes=sum(significant.elim))

kable(
   BP.all[BP.all$Significant > BP.all$Expected,],
   caption = "Most over-represented terms of the Biological Process ontology.")

Most over-represented terms of the Biological Process ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
1	GO:0001522	pseudouridine synthesis	31	4	1.57	2	0.0014	0.0014	0.00143
2	GO:0046854	phosphatidylinositol phosphorylation	45	4	2.27	4	0.0027	0.0027	0.00272
3	GO:0006400	tRNA modification	58	7	2.93	45	0.0163	0.0029	0.01633
4	GO:0050684	regulation of mRNA processing	15	3	0.76	12	0.0059	0.0038	0.00592
5	GO:0030513	positive regulation of BMP signaling pat…	9	4	0.45	8	0.0052	0.0052	0.00525
6	GO:0060271	cilium assembly	73	4	3.69	7	0.0049	0.0068	0.00038
7	GO:0016579	protein deubiquitination	90	9	4.55	14	0.0070	0.0070	0.00696
8	GO:0048015	phosphatidylinositol-mediated signaling	40	4	2.02	20	0.0081	0.0081	0.00806
9	GO:0070286	axonemal dynein complex assembly	9	1	0.45	21	0.0082	0.0082	0.00823
10	GO:0055072	iron ion homeostasis	21	3	1.06	622	0.4004	0.0094	0.40036
11	GO:0007411	axon guidance	11	3	0.56	27	0.0118	0.0118	0.01182
13	GO:0015937	coenzyme A biosynthetic process	8	1	0.40	41	0.0147	0.0147	0.01467
14	GO:0007275	multicellular organism development	85	7	4.29	108	0.0469	0.0155	0.00208
15	GO:0046434	organophosphate catabolic process	52	3	2.63	893	0.5923	0.0158	0.59232
16	GO:0060828	regulation of canonical Wnt signaling pa…	5	2	0.25	46	0.0168	0.0168	0.01683
18	GO:0006511	ubiquitin-dependent protein catabolic pr…	204	12	10.30	325	0.2086	0.0178	0.20864
20	GO:0048017	inositol lipid-mediated signaling	50	6	2.53	53	0.0188	0.0188	0.00241
21	GO:0006488	dolichol-linked oligosaccharide biosynth…	11	1	0.56	54	0.0189	0.0189	0.01886
22	GO:0006654	phosphatidic acid biosynthetic process	10	2	0.51	55	0.0189	0.0189	0.01887
23	GO:0007040	lysosome organization	8	2	0.40	58	0.0193	0.0193	0.01933

kable(
   BP.all[BP.all$Significant < BP.all$Expected,],
   caption = "Most under-represented terms of the Biological Process ontology.")

Most under-represented terms of the Biological Process ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
12	GO:0006418	tRNA aminoacylation for protein translat…	87	2	4.39	78	0.0333	0.0124	0.03332
17	GO:0050953	sensory perception of light stimulus	11	0	0.56	846	0.5527	0.0172	0.55272
19	GO:0032543	mitochondrial translation	5	0	0.25	52	0.0186	0.0186	0.01859
24	GO:0006030	chitin metabolic process	103	5	5.20	142	0.0681	0.0222	0.06805

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term = Term(GOTERM[sigTerms]),
                 Definition = Definition(GOTERM[sigTerms]),
                 PValue=score(BP.weight01)[sigTerms]),
      caption = paste('Biological process terms significantly associated with',
                      VAR, 'according to all 3 algorithms', sep=' '))

Biological process terms significantly associated with hatching according to all 3 algorithms

	Term	Definition	PValue
GO:0001522	pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.	0.0014295
GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.	0.0027221
GO:0050684	regulation of mRNA processing	Any process that modulates the frequency, rate or extent of mRNA processing, those processes involved in the conversion of a primary mRNA transcript into a mature mRNA prior to its translation into polypeptide.	0.0038049
GO:0030513	positive regulation of BMP signaling pathway	Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.	0.0052479
GO:0060271	cilium assembly	The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.	0.0067752
GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.	0.0069571
GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.	0.0080632
GO:0070286	axonemal dynein complex assembly	The aggregation, arrangement and bonding together of a set of components to form an axonemal dynein complex, a dynein complex found in eukaryotic cilia and flagella, in which the motor domain heads interact with adjacent microtubules to generate a sliding force which is converted to a bending motion.	0.0082319

I think the GO graph is useful to see the relationship among the significant terms. But too large graphs are impossible to read. I don’t know how to split the graph in meaningful subgraphs.

showSigOfNodes(GOdata.BP, score(BP.weight01),
               firstSigNodes = sum(significant.elim),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 276 
## Number of Edges = 533 
## 
## $complete.dag
## [1] "A graph with 276 nodes."

This is just a example of the most significant GO term:

showGroupDensity(GOdata.BP, names(score(BP.weight01))[which.min(score(BP.weight01))])

Molecular function

orderedTerms <- names(sort(score(MF.weight01)))
significant.weight01 <- score(MF.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(MF.lea)[orderedTerms] <= 0.01
significant.elim     <- score(MF.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
MF.pvalue.sigTerms <- sigTerms

MF.all <- GenTable(GOdata.MF, elim=MF.elim, weight01=MF.weight01, lea=MF.lea,
                   orderBy="weight01", ranksOf="elim", topNodes=sum(significant.elim))

kable(
   MF.all[MF.all$Significant > MF.all$Expected,],
   caption = "Most over-represented terms of the Molecular Function ontology.")

Most over-represented terms of the Molecular Function ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
1	GO:0016747	transferase activity, transferring acyl …	158	9	7.84	149	0.18300	0.00036	0.20455
3	GO:0035091	phosphatidylinositol binding	109	9	5.41	1	0.00025	0.00045	0.00025
5	GO:0005509	calcium ion binding	638	33	31.65	3	0.00156	0.00156	0.00156
7	GO:0009982	pseudouridine synthase activity	27	2	1.34	5	0.00300	0.00300	0.00300
9	GO:0060090	molecular adaptor activity	45	6	2.23	16	0.01539	0.00449	0.01539
10	GO:0005515	protein binding	4270	224	211.82	28	0.02495	0.00528	0.01108

kable(
   MF.all[MF.all$Significant < MF.all$Expected,],
   caption = "Most under-represented terms of the Molecular Function ontology.")

Most under-represented terms of the Molecular Function ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
2	GO:0140101	catalytic activity, acting on a tRNA	139	4	6.90	2	0.00096	0.00041	0.00096
4	GO:0004812	aminoacyl-tRNA ligase activity	90	2	4.46	17	0.01613	0.00098	0.01613
6	GO:0004594	pantothenate kinase activity	5	0	0.25	4	0.00283	0.00283	0.00283
8	GO:0008417	fucosyltransferase activity	42	2	2.08	6	0.00422	0.00422	0.00422

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term=Term(GOTERM[sigTerms]),
                 Definition=Definition(GOTERM[sigTerms]),
                 PValue=score(MF.weight01)[sigTerms]),
      caption = paste('Molecular function terms significantly associated with', VAR,
                      'according to all 3 algorithms', sep=' '))

Molecular function terms significantly associated with hatching according to all 3 algorithms

	Term	Definition	PValue
GO:0140101	catalytic activity, acting on a tRNA	NA	0.0004062
GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.	0.0004529
GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).	0.0015580
GO:0004594	pantothenate kinase activity	Catalysis of the reaction: ATP + pantothenate = ADP + D-4’-phosphopantothenate.	0.0028317
GO:0009982	pseudouridine synthase activity	Catalysis of the reaction: RNA uridine = RNA pseudouridine. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1’-N-1 glycosidic bond of uridine in RNA to a C1’-C5.	0.0030029
GO:0008417	fucosyltransferase activity	Catalysis of the transfer of a fucosyl group to an acceptor molecule, typically another carbohydrate or a lipid.	0.0042250
GO:0004630	phospholipase D activity	Catalysis of the reaction: a phosphatidylcholine + H2O = choline + a phosphatidate.	0.0059711

showSigOfNodes(GOdata.MF, score(MF.weight01),
               firstSigNodes = sum(significant.elim),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 38 
## Number of Edges = 41 
## 
## $complete.dag
## [1] "A graph with 38 nodes."

showGroupDensity(GOdata.MF, names(score(MF.weight01))[which.min(score(MF.weight01))])

Cellular component

orderedTerms <- names(sort(score(CC.weight01)))
significant.weight01 <- score(CC.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(CC.lea)[orderedTerms] <= 0.01
significant.elim     <- score(CC.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
CC.pvalue.sigTerms <- sigTerms

CC.all <- GenTable(GOdata.CC, elim=CC.elim, weight01=CC.weight01, lea=CC.lea,
                   orderBy="weight01", ranksOf="elim", topNodes=sum(significant.elim))
kable(
   CC.all[CC.all$Significant > CC.all$Expected,],
   caption = "Most over-represented terms of the Cellular Component ontology.")

Most over-represented terms of the Cellular Component ontology.

GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
GO:1902555	endoribonuclease complex	10	1	0.49	10	0.020	0.004	0.020
GO:0005576	extracellular region	197	13	9.56	15	0.026	0.014	0.026

kable(
   CC.all[CC.all$Significant < CC.all$Expected,],
   caption = "Most under-represented terms of the Cellular Component ontology.")

Most under-represented terms of the Cellular Component ontology.

GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term=Term(GOTERM[sigTerms]),
                 Definition=Definition(GOTERM[sigTerms]),
                 PValue=score(CC.weight01)[sigTerms]),
      caption = paste('Cellular component terms significantly associated with', VAR,
                      'according to all 3 algorithms', sep=' '))

Cellular component terms significantly associated with hatching according to all 3 algorithms

Term	Definition	PValue

showSigOfNodes(GOdata.CC, score(CC.weight01),
               firstSigNodes = sum(significant.elim),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 6 
## Number of Edges = 5 
## 
## $complete.dag
## [1] "A graph with 6 nodes."

showGroupDensity(GOdata.CC, names(score(CC.weight01))[which.min(score(CC.weight01))])

Using the portion of variance explained by hatching

Building the topGO object

I need to generate the topGO objects again, using the alternative gene ordering, based on the proportion of expression-level variance explained by hatching. I miss a way to inform the topGOdata object that the score in this case is reversed, with respect to p-values: the higher it is, the more differentially expressed the gene is. To make sure that GO terms are tested in the same way than when using p-values, I will just reverse the proportion of variance explained by hatching to its complement. Taking this into account, the subset of interesting genes (selection() function) must be defined as the lowest 10% scores, which are the 10% genes with largest portion of variance explained by hatching.

selection <- function(allScores) {return(allScores <= quantile(allScores, probs = 0.10))}
GOdataVar.BP <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'BP', 
   allGenes = 1.0 - Variance,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

GOdataVar.MF <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'MF',
   allGenes = 1.0 - Variance,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

GOdataVar.CC <- new('topGOdata',
   description = 'Differential expression among Brachionus plicatilis populations.',
   ontology = 'CC',
   allGenes = 1.0 - Variance,
   annot = annFUN.gene2GO,
   gene2GO = allgenes2GO,
   geneSelectionFun = selection,
   nodeSize = 5)

library(knitr)
DataSummary <- data.frame(ontology = c('BP', 'MF', 'CC'),
   Num_Genes = sapply(list(GOdataVar.BP, GOdataVar.MF, GOdataVar.CC), numGenes),
   Num_GO_terms = sapply(list(GOdataVar.BP, GOdataVar.MF, GOdataVar.CC), function(x) length(usedGO(x))))
kable(DataSummary, caption='Number of feasible genes or transcripts and number of GO terms used in each data set.')
rm(DataSummary)

Number of feasible genes or transcripts and number of GO terms used in each data set.

ontology	Num_Genes	Num_GO_terms
BP	26235	1582
MF	30580	791
CC	21616	390

Running the tests

BPvar.elim     <- runTest(GOdataVar.BP, algorithm = "elim",     statistic = "ks")
BPvar.weight01 <- runTest(GOdataVar.BP, algorithm = "weight01", statistic = "ks")
BPvar.lea      <- runTest(GOdataVar.BP, algorithm = "lea",      statistic = "ks")
MFvar.elim     <- runTest(GOdataVar.MF, algorithm = "elim",     statistic = "ks")
MFvar.weight01 <- runTest(GOdataVar.MF, algorithm = "weight01", statistic = "ks")
MFvar.lea      <- runTest(GOdataVar.MF, algorithm = "lea",      statistic = "ks")
CCvar.elim     <- runTest(GOdataVar.CC, algorithm = "elim",     statistic = "ks")
CCvar.weight01 <- runTest(GOdataVar.CC, algorithm = "weight01", statistic = "ks")
CCvar.lea      <- runTest(GOdataVar.CC, algorithm = "lea",      statistic = "ks")

ResultsSummary <- data.frame(ontology = rep(c("BP", "MF", "CC"), each = 3),
   algorithm = rep(c("elim", "weight01", "lea"), 3),
   TermsTested = sapply(list(BPvar.elim, BPvar.weight01, BPvar.lea, MFvar.elim, MFvar.weight01, MFvar.lea, CCvar.elim, CCvar.weight01, CCvar.lea), function(X) length(score(X))),
   Significant = sapply(list(BPvar.elim, BPvar.weight01, BPvar.lea, MFvar.elim, MFvar.weight01, MFvar.lea, CCvar.elim, CCvar.weight01, CCvar.lea), function(X) sum(score(X) < 0.01)))

kable(ResultsSummary, caption="Number of non-trivial terms tested and those with a score (not corrected p-value) lower than 0.01.")

Number of non-trivial terms tested and those with a score (not corrected p-value) lower than 0.01.

ontology	algorithm	TermsTested	Significant
BP	elim	1582	33
BP	weight01	1582	18
BP	lea	1582	66
MF	elim	791	23
MF	weight01	791	20
MF	lea	791	29
CC	elim	390	10
CC	weight01	390	3
CC	lea	390	18

rm(ResultsSummary)

Results

Biological process

orderedTerms <- names(sort(score(BPvar.weight01)))
significant.weight01 <- score(BPvar.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(BPvar.lea)[orderedTerms] <= 0.01
significant.elim     <- score(BPvar.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
BP.variance.sigTerms <- sigTerms

BPvar.all <- GenTable(GOdataVar.BP, elim=BPvar.elim, weight01=BPvar.weight01, lea=BPvar.lea,
                      orderBy="weight01", ranksOf="elim", topNodes=sum(significant.elim))

kable(
   BPvar.all[BPvar.all$Significant > BPvar.all$Expected,],
   caption = "Most over-represented terms of the Biological Process ontology.")

Most over-represented terms of the Biological Process ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
1	GO:0006511	ubiquitin-dependent protein catabolic pr…	204	33	20.21	9	0.00217	2.2e-05	0.00217
2	GO:0030513	positive regulation of BMP signaling pat…	9	3	0.89	1	3.6e-05	3.6e-05	3.6e-05
3	GO:0016579	protein deubiquitination	90	19	8.92	2	8.2e-05	8.2e-05	8.2e-05
5	GO:0007411	axon guidance	11	3	1.09	5	0.00074	0.00074	0.00074
6	GO:0007264	small GTPase mediated signal transductio…	228	31	22.59	10	0.00297	0.00123	0.00297
7	GO:0046434	organophosphate catabolic process	52	6	5.15	362	0.15812	0.00147	0.15812
8	GO:0032543	mitochondrial translation	5	1	0.50	8	0.00192	0.00192	0.00192
11	GO:0001522	pseudouridine synthesis	31	9	3.07	13	0.00328	0.00328	0.00328
12	GO:0006400	tRNA modification	58	12	5.75	59	0.01725	0.00335	0.01725
13	GO:0006997	nucleus organization	5	3	0.50	14	0.00342	0.00342	0.00342
14	GO:0035307	positive regulation of protein dephospho…	5	2	0.50	18	0.00516	0.00516	0.00516
16	GO:0046907	intracellular transport	422	60	41.81	139	0.04443	0.00660	0.00088
17	GO:0015937	coenzyme A biosynthetic process	8	3	0.79	24	0.00668	0.00668	0.00668
18	GO:0034474	U2 snRNA 3’-end processing	17	4	1.68	30	0.00915	0.00915	0.00915
20	GO:0006397	mRNA processing	158	35	15.65	12	0.00322	0.01045	0.00322
22	GO:0030163	protein catabolic process	241	35	23.87	7	0.00137	0.01230	5.1e-05
24	GO:0050953	sensory perception of light stimulus	11	2	1.09	824	0.46346	0.01444	0.46346
25	GO:0007029	endoplasmic reticulum organization	13	2	1.29	49	0.01522	0.01522	0.01522
26	GO:0038007	netrin-activated signaling pathway	5	1	0.50	50	0.01527	0.01527	0.01527
27	GO:0034314	Arp2/3 complex-mediated actin nucleation	17	4	1.68	52	0.01539	0.01539	0.01539
28	GO:0035195	gene silencing by miRNA	5	1	0.50	53	0.01546	0.01546	0.01546
29	GO:0070286	axonemal dynein complex assembly	9	2	0.89	56	0.01634	0.01634	0.01634
30	GO:0046854	phosphatidylinositol phosphorylation	45	11	4.46	63	0.01918	0.01918	0.01918
31	GO:0006904	vesicle docking involved in exocytosis	22	6	2.18	67	0.01959	0.01959	0.01959
33	GO:0051270	regulation of cellular component movemen…	5	1	0.50	68	0.01975	0.01975	0.01975

kable(
   BPvar.all[BPvar.all$Significant < BPvar.all$Expected,],
   caption = "Most under-represented terms of the Biological Process ontology.")

Most under-represented terms of the Biological Process ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
4	GO:0055072	iron ion homeostasis	21	2	2.08	514	0.24052	0.00011	0.24052
9	GO:0006030	chitin metabolic process	103	10	10.20	21	0.00606	0.00202	0.00606
10	GO:0006486	protein glycosylation	106	10	10.50	6	0.00083	0.00292	0.00083
15	GO:0060271	cilium assembly	73	6	7.23	3	0.00039	0.00532	0.00039
19	GO:0006545	glycine biosynthetic process	7	0	0.69	34	0.01016	0.01016	0.01016
21	GO:0010972	negative regulation of G2/M transition o…	5	0	0.50	37	0.01103	0.01103	0.01103
23	GO:1903047	mitotic cell cycle process	86	8	8.52	631	0.32396	0.01245	0.65910
32	GO:0006418	tRNA aminoacylation for protein translat…	87	7	8.62	60	0.01839	0.01962	0.01839

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term=Term(GOTERM[sigTerms]),
                 Definition=Definition(GOTERM[sigTerms]),
                 PValue=score(BPvar.weight01)[sigTerms]),
      caption = paste('Biological process terms significantly associated with', VAR,
                      'according to all 3 algorithms', sep=' '))

Biological process terms significantly associated with hatching according to all 3 algorithms

	Term	Definition	PValue
GO:0006511	ubiquitin-dependent protein catabolic process	The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.	0.0000222
GO:0030513	positive regulation of BMP signaling pathway	Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.	0.0000357
GO:0016579	protein deubiquitination	The removal of one or more ubiquitin groups from a protein.	0.0000819
GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.	0.0007397
GO:0007264	small GTPase mediated signal transduction	Any series of molecular signals in which a small monomeric GTPase relays one or more of the signals.	0.0012329
GO:0032543	mitochondrial translation	The chemical reactions and pathways resulting in the formation of a protein in a mitochondrion. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein; the mitochondrion has its own ribosomes and transfer RNAs, and uses a genetic code that differs from the nuclear code.	0.0019207
GO:0006030	chitin metabolic process	The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.	0.0020236
GO:0006486	protein glycosylation	A protein modification process that results in the addition of a carbohydrate or carbohydrate derivative unit to a protein amino acid, e.g. the addition of glycan chains to proteins.	0.0029192
GO:0001522	pseudouridine synthesis	The intramolecular conversion of uridine to pseudouridine within an RNA molecule. This posttranscriptional base modification occurs in tRNA, rRNA, and snRNAs.	0.0032848
GO:0006997	nucleus organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus.	0.0034201
GO:0035307	positive regulation of protein dephosphorylation	Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.	0.0051619
GO:0060271	cilium assembly	The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole.	0.0053173
GO:0015937	coenzyme A biosynthetic process	The chemical reactions and pathways resulting in the formation of coenzyme A, 3’-phosphoadenosine-(5’)diphospho(4’)pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.	0.0066754
GO:0034474	U2 snRNA 3’-end processing	Any process involved in forming the mature 3’ end of a U2 snRNA molecule.	0.0091518

showSigOfNodes(GOdataVar.BP, score(BPvar.weight01),
               firstSigNodes = sum(significant.elim),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 381 
## Number of Edges = 772 
## 
## $complete.dag
## [1] "A graph with 381 nodes."

Below I plot variance portion, but for the termo found most significant when using p-values, for comparison.

showGroupDensity(GOdataVar.BP, names(score(BP.weight01))[which.min(score(BP.weight01))])

Molecular function

orderedTerms <- names(sort(score(MFvar.weight01)))
significant.weight01 <- score(MFvar.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(MFvar.lea)[orderedTerms] <= 0.01
significant.elim     <- score(MFvar.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
MF.variance.sigTerms <- sigTerms

MFvar.all <- GenTable(GOdataVar.MF, elim=MFvar.elim, weight01=MFvar.weight01, lea=MFvar.lea,
                      orderBy="weight01", ranksOf="elim", topNodes=sum(significant.elim))
kable(
   MFvar.all[MFvar.all$Significant > MFvar.all$Expected,],
   caption = "Most over-represented terms of the Molecular Function ontology.")

Most over-represented terms of the Molecular Function ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
1	GO:0005515	protein binding	4270	487	418.76	4	0.00056	5.9e-05	0.00056
2	GO:0036459	thiol-dependent ubiquitinyl hydrolase ac…	103	23	10.10	1	3e-05	6.7e-05	3e-05
4	GO:0035091	phosphatidylinositol binding	109	23	10.69	2	0.00033	0.00055	0.00033
6	GO:0004298	threonine-type endopeptidase activity	31	4	3.04	6	0.00087	0.00087	0.00087
7	GO:0140101	catalytic activity, acting on a tRNA	139	16	13.63	10	0.00161	0.00118	0.00161
9	GO:0004594	pantothenate kinase activity	5	2	0.49	9	0.00142	0.00142	0.00142
10	GO:0003676	nucleic acid binding	2125	239	208.40	3	0.00052	0.00238	0.00052
11	GO:0016417	S-acyltransferase activity	6	4	0.59	11	0.00247	0.00247	0.00247
12	GO:0016742	hydroxymethyl-, formyl- and related tran…	9	3	0.88	13	0.00276	0.00276	0.00276
13	GO:0016887	ATPase activity	327	43	32.07	212	0.24838	0.00715	0.24838
15	GO:0060090	molecular adaptor activity	45	13	4.41	7	0.00121	0.00840	0.00121
16	GO:0005220	inositol 1,4,5-trisphosphate-sensitive c…	15	2	1.47	18	0.00879	0.00879	0.00879
17	GO:0070679	inositol 1,4,5 trisphosphate binding	15	2	1.47	19	0.00879	0.00879	0.00879
18	GO:0005516	calmodulin binding	52	10	5.10	20	0.00948	0.00948	0.00948
19	GO:0003993	acid phosphatase activity	10	1	0.98	22	0.00974	0.00974	0.00974
20	GO:0004312	fatty acid synthase activity	6	3	0.59	23	0.00998	0.00998	0.00998
21	GO:0046527	glucosyltransferase activity	17	4	1.67	16	0.00693	0.01026	0.00693
22	GO:0005102	signaling receptor binding	47	7	4.61	112	0.13378	0.01048	0.13378
23	GO:0016748	succinyltransferase activity	5	3	0.49	24	0.01065	0.01065	0.01065

kable(
   MFvar.all[MFvar.all$Significant < MFvar.all$Expected,],
   caption = "Most under-represented terms of the Molecular Function ontology.")

Most under-represented terms of the Molecular Function ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
3	GO:0038023	signaling receptor activity	471	34	46.19	325	0.41565	0.00025	0.48567
5	GO:0008061	chitin binding	112	10	10.98	5	0.00061	0.00061	0.00061
8	GO:0008417	fucosyltransferase activity	42	4	4.12	8	0.00136	0.00136	0.00136
14	GO:0004812	aminoacyl-tRNA ligase activity	90	7	8.83	42	0.03055	0.00828	0.03055

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term=Term(GOTERM[sigTerms]),
                 Definition=Definition(GOTERM[sigTerms]),
                 PValue=score(MFvar.weight01)[sigTerms]),
      caption = paste('Molecular functions terms significantly associated with', VAR,
                      'according to all 3 algorithms', sep=' '))

Molecular functions terms significantly associated with hatching according to all 3 algorithms

	Term	Definition	PValue
GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).	0.0000586
GO:0036459	thiol-dependent ubiquitinyl hydrolase activity	Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.	0.0000670
GO:0035091	phosphatidylinositol binding	Interacting selectively and non-covalently with any inositol-containing glycerophospholipid, i.e. phosphatidylinositol (PtdIns) and its phosphorylated derivatives.	0.0005496
GO:0008061	chitin binding	Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.	0.0006105
GO:0004298	threonine-type endopeptidase activity	Catalysis of the hydrolysis of internal peptide bonds in a polypeptide chain by a mechanism in which the hydroxyl group of a threonine residue at the active center acts as a nucleophile.	0.0008677
GO:0140101	catalytic activity, acting on a tRNA	NA	0.0011815
GO:0008417	fucosyltransferase activity	Catalysis of the transfer of a fucosyl group to an acceptor molecule, typically another carbohydrate or a lipid.	0.0013571
GO:0004594	pantothenate kinase activity	Catalysis of the reaction: ATP + pantothenate = ADP + D-4’-phosphopantothenate.	0.0014241
GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.	0.0023808
GO:0016417	S-acyltransferase activity	Catalysis of the transfer of an acyl group to a sulfur atom on the acceptor molecule.	0.0024717
GO:0016742	hydroxymethyl-, formyl- and related transferase activity	Catalysis of the transfer of a hydroxymethyl- or formyl group from one compound (donor) to another (acceptor).	0.0027562
GO:0060090	molecular adaptor activity	The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.	0.0083968
GO:0005220	inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity	Enables the transmembrane transfer of a calcium ion by a channel that opens when inositol 1,4,5-trisphosphate (IP3) has been bound by the channel complex or one of its constituent parts.	0.0087864
GO:0070679	inositol 1,4,5 trisphosphate binding	Interacting selectively and non-covalently with inositol 1,4,5 trisphosphate.	0.0087864
GO:0005516	calmodulin binding	Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.	0.0094780
GO:0003993	acid phosphatase activity	Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an acid pH optimum.	0.0097424
GO:0004312	fatty acid synthase activity	Catalysis of the reaction: acetyl-CoA + n malonyl-CoA + 2n NADPH + 2n H+ = long-chain fatty acid + n+1 CoA + n CO2 + 2n NADP+.	0.0099792

showSigOfNodes(GOdataVar.MF, score(MFvar.weight01),
               firstSigNodes = sum(significant.elim),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 87 
## Number of Edges = 107 
## 
## $complete.dag
## [1] "A graph with 87 nodes."

I plot variance portion, but for the term found most significant when using p-values, for comparison.

showGroupDensity(GOdataVar.MF, names(score(MF.weight01))[which.min(score(MF.weight01))])

Cellular component

orderedTerms <- names(sort(score(CCvar.weight01)))
significant.weight01 <- score(CCvar.weight01)[orderedTerms] <= 0.01
significant.lea      <- score(CCvar.lea)[orderedTerms] <= 0.01
significant.elim     <- score(CCvar.elim)[orderedTerms] <= 0.01
sigTerms <- orderedTerms[significant.weight01 & significant.lea & significant.elim]
if (length(sigTerms) == 0) {
   sigTerms <- orderedTerms[significant.lea & significant.elim]
}
# sigTerms gets updated, and is already used in the code, but I need a permanent copy for later.
CC.variance.sigTerms <- sigTerms

CCvar.all <- GenTable(GOdataVar.CC, elim=CCvar.elim, weight01=CCvar.weight01, lea=CCvar.lea,
                      orderBy="weight01", ranksOf="elim", topNodes=max(sum(significant.elim), 10))

kable(
   CCvar.all[CCvar.all$Significant > CCvar.all$Expected,],
   caption = "Most over-represented terms of the Cellular Component ontology.")

Most over-represented terms of the Cellular Component ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
2	GO:0005737	cytoplasm	1176	121	110.82	22	0.0242	0.0073	0.00071
3	GO:0045239	tricarboxylic acid cycle enzyme complex	5	3	0.47	10	0.0100	0.0100	0.00996
4	GO:0005815	microtubule organizing center	96	15	9.05	28	0.0286	0.0105	0.15049
5	GO:1902555	endoribonuclease complex	10	3	0.94	46	0.0602	0.0105	0.06022
6	GO:0005761	mitochondrial ribosome	18	4	1.70	3	0.0035	0.0111	0.00347
7	GO:0005576	extracellular region	197	21	18.56	27	0.0282	0.0130	0.02818
8	GO:0030015	CCR4-NOT core complex	15	3	1.41	13	0.0153	0.0153	0.01528
10	GO:0031981	nuclear lumen	280	37	26.39	24	0.0253	0.0162	0.02534

kable(
   CCvar.all[CCvar.all$Significant < CCvar.all$Expected,],
   caption = "Most under-represented terms of the Cellular Component ontology.")

Most under-represented terms of the Cellular Component ontology.

	GO.ID	Term	Annotated	Significant	Expected	Rank in elim	elim	weight01	lea
1	GO:0016272	prefoldin complex	7	0	0.66	6	0.0053	0.0053	0.00531
9	GO:0005802	trans-Golgi network	12	1	1.13	14	0.0158	0.0158	0.01577

vennDiagram(vennCounts(cbind(weight01=significant.weight01,
                             lea=significant.lea,
                             elim=significant.elim)))

kable(data.frame(Term=Term(GOTERM[sigTerms]),
                 Definition=Definition(GOTERM[sigTerms]),
                 PValue=score(CCvar.weight01)[sigTerms]),
      caption = paste('Cellular component terms significantly associated with', VAR,
                      'according to all 3 algorithms', sep=' '))

Cellular component terms significantly associated with hatching according to all 3 algorithms

	Term	Definition	PValue
GO:0016272	prefoldin complex	A multisubunit chaperone that is capable of delivering unfolded proteins to cytosolic chaperonin, which it acts as a cofactor for. In humans, the complex is a heterohexamer of two PFD-alpha and four PFD-beta type subunits. In Saccharomyces cerevisiae, it also acts in the nucleus to regulate the rate of elongation by RNA polymerase II via a direct effect on histone dynamics.	0.0053057
GO:0045239	tricarboxylic acid cycle enzyme complex	Any of the heteromeric enzymes that act in the TCA cycle.	0.0099588

showSigOfNodes(GOdataVar.CC, score(CCvar.weight01),
               firstSigNodes = sum(significant.weight01),
               wantedNodes = sigTerms)

## $dag
## A graphNEL graph with directed edges
## Number of Nodes = 10 
## Number of Edges = 13 
## 
## $complete.dag
## [1] "A graph with 10 nodes."

For comparison, I plot the distribution of variance portion for the CC term found most significant when using p-values.

showGroupDensity(GOdataVar.CC, names(score(CC.weight01))[which.min(score(CC.weight01))])

Comparison between the two ordering of genes.

Biological process

allTerms <- usedGO(GOdata.BP)
vennDiagram(vennCounts(cbind(PValue   = allTerms %in% BP.pvalue.sigTerms,
                             Variance = allTerms %in% BP.variance.sigTerms)))

ggplot(data = data.frame(PValue   = rank(score(BP.weight01))[allTerms],
                         Variance = rank(score(BPvar.weight01))[allTerms]),
       mapping = aes(x = PValue, y = Variance)) +
   geom_point() + geom_smooth() + xlab('Using gene p-values') +
   ylab('Using portion of explained variance') +
   ggtitle('Ordering of BP terms by significance')

Molecular function

allTerms <- usedGO(GOdata.MF)
vennDiagram(vennCounts(cbind(PValue   = allTerms %in% MF.pvalue.sigTerms,
                             Variance = allTerms %in% MF.variance.sigTerms)))

ggplot(data = data.frame(PValue   = rank(score(MF.weight01))[allTerms],
                         Variance = rank(score(MFvar.weight01))[allTerms]),
       mapping = aes(x = PValue, y = Variance)) +
   geom_point() + geom_smooth() + xlab('Using gene p-values') +
   ylab('Using portion of explained variance') +
   ggtitle('Ordering of MF terms by significance')

Cellular component

allTerms <- usedGO(GOdata.CC)
vennDiagram(vennCounts(cbind(PValue   = allTerms %in% CC.pvalue.sigTerms,
                             Variance = allTerms %in% CC.variance.sigTerms)))

ggplot(data = data.frame(PValue   = rank(score(CC.weight01))[allTerms],
                         Variance = rank(score(CCvar.weight01))[allTerms]),
       mapping = aes(x = PValue, y = Variance)) +
   geom_point() + geom_smooth() + xlab('Using gene p-values') +
   ylab('Using portion of explained variance') +
   ggtitle('Ordering of CC terms by significance')

Session info

I save the main variables to be able to load them in a new R session later.

save(allgenes2GO,
     GOdata.BP, BP.elim, BP.weight01, BP.lea, BP.pvalue.sigTerms,
     GOdata.MF, MF.elim, MF.weight01, MF.lea, MF.pvalue.sigTerms,
     GOdata.CC, CC.elim, CC.weight01, CC.lea, CC.pvalue.sigTerms,
     GOdataVar.BP, BPvar.elim, BPvar.weight01, BPvar.lea, BP.variance.sigTerms,
     GOdataVar.MF, MFvar.elim, MFvar.weight01, MFvar.lea, MF.variance.sigTerms,
     GOdataVar.CC, CCvar.elim, CCvar.weight01, CCvar.lea, CC.variance.sigTerms,
     file = paste('Enrichment', TAG, VAR, 'RData', sep='.'))
sessionInfo()

## R version 3.6.2 (2019-12-12)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
## 
## Matrix products: default
## BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
## 
## locale:
##  [1] LC_CTYPE=ca_ES.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=ca_ES.UTF-8    
##  [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=ca_ES.UTF-8   
##  [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] Rgraphviz_2.30.0     ggplot2_3.2.1        limma_3.42.0        
##  [4] knitr_1.27           topGO_2.38.1         SparseM_1.78        
##  [7] GO.db_3.10.0         AnnotationDbi_1.48.0 IRanges_2.20.2      
## [10] S4Vectors_0.24.3     Biobase_2.46.0       graph_1.64.0        
## [13] BiocGenerics_0.32.0 
## 
## loaded via a namespace (and not attached):
##  [1] tidyselect_0.2.5   xfun_0.12          purrr_0.3.3        splines_3.6.2     
##  [5] lattice_0.20-38    colorspace_1.4-1   vctrs_0.2.1        htmltools_0.4.0   
##  [9] yaml_2.2.0         mgcv_1.8-31        blob_1.2.1         rlang_0.4.2       
## [13] pillar_1.4.3       glue_1.3.1         withr_2.1.2        DBI_1.1.0         
## [17] bit64_0.9-7        matrixStats_0.55.0 lifecycle_0.1.0    stringr_1.4.0     
## [21] munsell_0.5.0      gtable_0.3.0       memoise_1.1.0      evaluate_0.14     
## [25] labeling_0.3       highr_0.8          Rcpp_1.0.3         backports_1.1.5   
## [29] scales_1.1.0       farver_2.0.3       bit_1.1-15.1       digest_0.6.23     
## [33] stringi_1.4.5      dplyr_0.8.3        tools_3.6.2        magrittr_1.5      
## [37] lazyeval_0.2.2     tibble_2.1.3       RSQLite_2.2.0      crayon_1.3.4      
## [41] pkgconfig_2.0.3    zeallot_0.1.0      Matrix_1.2-18      assertthat_0.2.1  
## [45] rmarkdown_2.1      R6_2.4.1           nlme_3.1-143       compiler_3.6.2